Terminal modification, sequence, length, and PIWI-protein identity determine piRNA stability

Ago2 protects Drosophila siRNAs and microRNAs from target-directed degradation, even in the absence of 2′-O-methylation

(2021) Elena R. Kingston et al.   RNA

Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA

(2021) Heejin Choi et al.   PLoS Genetics

Structural basis for piRNA targeting

(2021) Todd A. Anzelon et al.   NATURE

pre-piRNA trimming and 2′-O-methylation protect piRNAs from 3′ tailing and degradation in C. elegans

(2021) Benjamin Pastore et al.   Cell Reports

Zucchini consensus motifs determine the mechanism of pre-piRNA production

(2020) Natsuko Izumi et al.   NATURE

Crystal structure of Drosophila Piwi

(2020) Sonomi Yamaguchi et al.   Nature Communications

Evolutionarily conserved pachytene piRNA loci are highly divergent among modern humans

(2020) Deniz M. Özata et al.   Nature Ecology & Evolution

The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility

(2020) Pei-Hsuan Wu et al.   NATURE GENETICS

Structure-function analysis of microRNA 3′-end trimming by Nibbler

(2020) Wei Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A programmed wave of uridylation-primed mRNA degradation is essential for meiotic progression and mammalian spermatogenesis

(2019) Marcos Morgan et al.   CELL RESEARCH

Daedalus and Gasz recruit Armitage to mitochondria, bringing piRNA precursors to the biogenesis machinery

(2019) Marzia Munafò et al.   GENES & DEVELOPMENT

The RNA-Binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on Mitochondria

(2019) Daniel Tianfang Ge et al.   MOLECULAR CELL

Distinct and Collaborative Functions of Yb and Armitage in Transposon-Targeting piRNA Biogenesis

(2019) Hirotsugu Ishizu et al.   Cell Reports

Structural Basis for Target-Directed MicroRNA Degradation

(2019) Jessica Sheu-Gruttadauria et al.   MOLECULAR CELL

Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis

(2019) Brian Reichholf et al.   MOLECULAR CELL

Global analyses of the dynamics of mammalian microRNA metabolism

(2019) Elena Kingston et al.   GENOME RESEARCH

microRNA arm-imbalance in part from complementary targets mediated decay promotes gastric cancer progression

(2019) Zhengyi Zhang et al.   Nature Communications

henn-1/HEN1 Promotes Germline Immortality in Caenorhabditis elegans

(2019) Joshua M. Svendsen et al.   Cell Reports

Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

(2018) Yu Fu et al.   BMC GENOMICS

A Network of Noncoding Regulatory RNAs Acts in the Mammalian Brain

(2018) Benjamin Kleaveland et al.   CELL

Metazoan MicroRNAs

(2018) David P. Bartel   CELL

PNLDC1, mouse pre‐piRNA Trimmer, is required for meiotic and post‐meiotic male germ cell development

(2018) Toru Nishimura et al.   EMBO REPORTS

Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos

(2018) Hyeshik Chang et al.   MOLECULAR CELL

MicroRNA degradation by a conserved target RNA regulates animal behavior

(2018) Angelo Bitetti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MicroRNA degradation by a conserved target RNA regulates animal behavior

(2018) Angelo Bitetti et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biology

(2018) Yu Fu et al.   eLife

A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most Animals

(2018) Ildar Gainetdinov et al.   MOLECULAR CELL

Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation

(2018) Francesco Ghini et al.   Nature Communications

The methyltransferase HEN1 is required in Nematostella vectensis for microRNA and piRNA stability as well as larval metamorphosis

(2018) Vengamanaidu Modepalli et al.   PLoS Genetics

piRNA-Guided Genome Defense: From Biogenesis to Silencing

(2018) Benjamin Czech et al.   Annual Review of Genetics

Iruka Eliminates Dysfunctional Argonaute by Selective Ubiquitination of Its Empty State

(2018) Hotaka Kobayashi et al.   MOLECULAR CELL

PIWI-interacting RNAs: small RNAs with big functions

(2018) Deniz M. Ozata et al.   NATURE REVIEWS GENETICS

Mitochondrial membrane-based initial separation of MIWI and MILI functions during pachytene piRNA biogenesis

(2018) Deqiang Ding et al.   NUCLEIC ACIDS RESEARCH

The multitasking polyA tail: nuclear RNA maturation, degradation and export

(2018) Agnieszka Tudek et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The role of 3′ end uridylation in RNA metabolism and cellular physiology

(2018) Dagmar Zigáčková et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TimeTree: A Resource for Timelines, Timetrees, and Divergence Times

(2017) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

mRNA 3′ uridylation and poly(A) tail length sculpt the mammalian maternal transcriptome

(2017) Marcos Morgan et al.   NATURE

Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis

(2017) Christopher R Faehnle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

piRNA Biogenesis in Drosophila melanogaster

(2017) Xiawei Huang et al.   TRENDS IN GENETICS

PNLDC1 is essential for piRNA 3′ end trimming and transposon silencing during spermatogenesis in mice

(2017) Deqiang Ding et al.   Nature Communications

Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis

(2017) Christopher R Faehnle et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements

(2017) Samuel H. Lewis et al.   Nature Ecology & Evolution

Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA

(2016) Naoki Matsumoto et al.   CELL

The RNase PARN-1 Trims piRNA 3′ Ends to Promote Transcriptome Surveillance in C. elegans

(2016) Wen Tang et al.   CELL

Identification and Functional Analysis of the Pre-piRNA 3′ Trimmer in Silkworms

(2016) Natsuko Izumi et al.   CELL

Molecular basis for cytoplasmic RNA surveillance by uridylation‐triggered decay in Drosophila

(2016) Madalena M Reimão‐Pinto et al.   EMBO JOURNAL

TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs

(2016) Dmytro Ustianenko et al.   EMBO JOURNAL

Degradation dynamics of microRNAs revealed by a novel pulse-chase approach

(2016) Matteo J. Marzi et al.   GENOME RESEARCH

Genetic and mechanistic diversity of piRNA 3′-end formation

(2016) Rippei Hayashi et al.   NATURE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

MIWI2 as an Effector of DNA Methylation and Gene Silencing in Embryonic Male Germ Cells

(2016) Kanako Kojima-Kita et al.   Cell Reports

The exonuclease Nibbler regulates age-associated traits and modulates piRNA length inDrosophila

(2015) Virzhiniya L. Feltzin et al.   AGING CELL

MIWI and piRNA-mediated cleavage of messenger RNAs in mouse testes

(2015) Peng Zhang et al.   CELL RESEARCH

TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms

(2015) B. Kim et al.   EMBO JOURNAL

Potent degradation of neuronal miRNAs induced by highly complementary targets

(2015) M. de la Mata et al.   EMBO REPORTS

piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis

(2015) Wee Siong Sho Goh et al.   GENES & DEVELOPMENT

Tracking Distinct RNA Populations Using Efficient and Reversible Covalent Chemistry

(2015) Erin E. Duffy et al.   MOLECULAR CELL

Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs

(2015) Min-Te Chou et al.   NUCLEIC ACIDS RESEARCH

piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis

(2015) F. Mohn et al.   SCIENCE

piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production

(2015) B. W. Han et al.   SCIENCE

PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis

(2015) David Homolka et al.   Cell Reports

HENMT1 and piRNA Stability Are Required for Adult Male Germ Cell Transposon Repression and to Define the Spermatogenic Program in the Mouse

(2015) Shu Ly Lim et al.   PLoS Genetics

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

Uridylation by TUT4 and TUT7 Marks mRNA for Degradation

(2014) Jaechul Lim et al.   CELL

Cnidarian microRNAs frequently regulate targets by cleavage

(2014) Y. Moran et al.   GENOME RESEARCH

The Initial Uridine of Primary piRNAs Does Not Create the Tenth Adenine that Is the Hallmark of Secondary piRNAs

(2014) Wei Wang et al.   MOLECULAR CELL

Mechanism of Dis3l2 substrate recognition in the Lin28–let-7 pathway

(2014) Christopher R. Faehnle et al.   NATURE

The MID-PIWI module of Piwi proteins specifies nucleotide- and strand-biases of piRNAs

(2014) E. Cora et al.   RNA

Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference

(2014) Delphine Potier et al.   Cell Reports

Selective Degradation of Host MicroRNAs by an Intergenic HCMV Noncoding RNA Accelerates Virus Production

(2013) Sanghyun Lee et al.   Cell Host & Microbe

Analysis of Hydra PIWI proteins and piRNAs uncover early evolutionary origins of the piRNA pathway

(2013) Robyn S.M. Lim et al.   DEVELOPMENTAL BIOLOGY

Tdrkh is essential for spermatogenesis and participates in primary piRNA biogenesis in the germline

(2013) Jonathan P Saxe et al.   EMBO JOURNAL

The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway

(2013) Michal Malecki et al.   EMBO JOURNAL

An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28–let-7 pathway

(2013) Hao-Ming Chang et al.   NATURE

Homeostatic control of Argonaute stability by microRNA availability

(2013) Peter Smibert et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PIWI proteins and PIWI-interacting RNAs function in Hydra somatic stem cells

(2013) C. E. Juliano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The co-chaperones Fkbp4/5 control Argonaute2 expression and facilitate RISC assembly

(2013) N. J. Martinez et al.   RNA

Mammalian DIS3L2 exoribonuclease targets the uridylated precursors of let-7 miRNAs

(2013) D. Ustianenko et al.   RNA

Argonaute2 expression is post-transcriptionally coupled to microRNA abundance

(2013) N. J. Martinez et al.   RNA

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Degradation of Host MicroRNAs by Poxvirus Poly(A) Polymerase Reveals Terminal RNA Methylation as a Protective Antiviral Mechanism

(2012) Simone Backes et al.   Cell Host & Microbe

Structure and function of Zucchini endoribonuclease in piRNA biogenesis

(2012) Hiroshi Nishimasu et al.   NATURE

The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis

(2012) Jonathan J. Ipsaro et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Degradation of the antiviral component ARGONAUTE1 by the autophagy pathway

(2012) B. Derrien et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lin28-mediated control of let-7 microRNA expression by alternative TUTases Zcchc11 (TUT4) and Zcchc6 (TUT7)

(2012) J. E. Thornton et al.   RNA

MicroRNA turnover: when, how, and why

(2012) Stefan Rüegger et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs

(2012) Allison C. Billi et al.   PLoS Genetics

PIWI Associated siRNAs and piRNAs Specifically Require the Caenorhabditis elegans HEN1 Ortholog henn-1

(2012) Taiowa A. Montgomery et al.   PLoS Genetics

Differential Impact of the HEN1 Homolog HENN-1 on 21U and 26G RNAs in the Germline of Caenorhabditis elegans

(2012) Leonie M. Kamminga et al.   PLoS Genetics

Degradation of Cellular miR-27 by a Novel, Highly Abundant Viral Transcript Is Important for Efficient Virus Replication In Vivo

(2012) Lisa Marcinowski et al.   PLoS Pathogens

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

The Exoribonuclease Nibbler Controls 3′ End Processing of MicroRNAs in Drosophila

(2011) Nan Liu et al.   CURRENT BIOLOGY

Kinetic Analysis Reveals the Fate of a MicroRNA following Target Regulation in Mammalian Cells

(2011) Alessia Baccarini et al.   CURRENT BIOLOGY

The 3′-to-5′ Exoribonuclease Nibbler Shapes the 3′ Ends of MicroRNAs Bound to Drosophila Argonaute1

(2011) Bo W. Han et al.   CURRENT BIOLOGY

Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila

(2011) A. L. Zamparini et al.   DEVELOPMENT

MITOPLD Is a Mitochondrial Protein Essential for Nuage Formation and piRNA Biogenesis in the Mouse Germline

(2011) Toshiaki Watanabe et al.   DEVELOPMENTAL CELL

piRNA-Associated Germline Nuage Formation and Spermatogenesis Require MitoPLD Profusogenic Mitochondrial-Surface Lipid Signaling

(2011) Huiyan Huang et al.   DEVELOPMENTAL CELL

3′ End Formation of PIWI-Interacting RNAs In Vitro

(2011) Shinpei Kawaoka et al.   MOLECULAR CELL

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing

(2011) Michael Reuter et al.   NATURE

Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target

(2011) V. Libri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Hen1 is required for oocyte development and piRNA stability in zebrafish

(2010) Leonie M Kamminga et al.   EMBO JOURNAL

Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila

(2010) A. D. Haase et al.   GENES & DEVELOPMENT

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway

(2010) K. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

(2010) R. J. A. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Down-Regulation of a Host MicroRNA by a Herpesvirus saimiri Noncoding RNA

(2010) D. Cazalla et al.   SCIENCE

Target RNA-Directed Trimming and Tailing of Small Silencing RNAs

(2010) S. L. Ameres et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

TUT4 in Concert with Lin28 Suppresses MicroRNA Biogenesis through Pre-MicroRNA Uridylation

(2009) Inha Heo et al.   CELL

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Gtsf1/Cue110, a gene encoding a protein with two copies of a CHHC Zn-finger motif, is involved in spermatogenesis and retrotransposon suppression in murine testes

(2009) Takuji Yoshimura et al.   DEVELOPMENTAL BIOLOGY

The TDRD9-MIWI2 Complex Is Essential for piRNA-Mediated Retrotransposon Silencing in the Mouse Male Germline

(2009) Masanobu Shoji et al.   DEVELOPMENTAL CELL

Isolation of mitochondria-associated membranes and mitochondria from animal tissues and cells

(2009) Mariusz R Wieckowski et al.   Nature Protocols

Decapping is preceded by 3′ uridylation in a novel pathway of bulk mRNA turnover

(2009) Olivia S Rissland et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

2'-O-methylation stabilizes Piwi-associated small RNAs and ensures DNA elimination in Tetrahymena

(2009) H. M. Kurth et al.   RNA

GASZ Is Essential for Male Meiosis and Suppression of Retrotransposon Expression in the Male Germline

(2009) Lang Ma et al.   PLoS Genetics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Mouse Maelstrom, a Component of Nuage, Is Essential for Spermatogenesis and Transposon Repression in Meiosis

(2008) Sarah F.C. Soper et al.   DEVELOPMENTAL CELL

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

PRG-1 and 21U-RNAs Interact to Form the piRNA Complex Required for Fertility in C. elegans

(2008) Pedro J. Batista et al.   MOLECULAR CELL

Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals

(2008) Andrew Grimson et al.   NATURE